Question: (Closed) How to use cummeRbund to draw plots after processing cuffdiff? (cuffdiff does not output .sqlite file as it should)
gravatar for yusheng_tan
13 months ago by
yusheng_tan0 wrote:


I created a workflow having Cuffdiff in the end, which outputs the last file, .sqlite file, to serve the CummeRbund. However, it does not work. No .sqlite file was output. Even though after that I added the module of CummeRbund in the workflow, connected with Cuffdiff, it just does not work. Still, no .sqlite file was output and no result for cummeRbund.

So I wonder the method to output .sqlite file though Cuffdiff and then plot the DEGs results in CummeRbund and how it could work like in a workflow.

Thank you so much.

Have a good day, Yusheng

rna-seq galaxy cufflinks • 859 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by yusheng_tan0

Hello yusheng_tan!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


What version of Galaxy is your server and what version of Cuffdiff did you install?

An earlier version of Cuffdiff is installed at (and the SQlite function works).

We will upgrading/testing to the version (the most current version in the Tool Shed). As far as I know, there are no issues with it reported so far with respect to this function.

But, please follow here for updates and testing of the latest version in the latest version of Galaxy (a pre-release version of 17.09):

For now, double check the install and consider using the earlier version if you need to do this work right now. Or, wait and follow the testing of the newer version and then use once is confirmed to be successful.

Thanks for reporting the problem, Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k

Update: The SQLite option has been confirmed to be problematic with Cuffdiff at Please follow the same ticket above for updates.

Meanwhile, Cuffdiff can be used. If the failed job's tool form is brought up using the rerun button, you can switch using the Versions menu at the top of the form and the original data will populate into that tool form. Or, you can just start over using the tool directly from the tool panel.

If you are working at your own server, install the version.

ADD REPLYlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k
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